-
Notifications
You must be signed in to change notification settings - Fork 6
/
README
41 lines (21 loc) · 2.89 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
# **NeatSeq-Flow**: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows.
<img src="https://github.com/bioinfo-core-BGU/neatseq-flow/blob/master/doc/source/figs/NeatSeq_Flow_logo.png" width="400">
[](http://neatseq-flow-modules.readthedocs.io/en/latest/?badge=latest)
# Additional NeatSeq-Flow modules
This repository includes modules that extend the functionality of NeatSeq-Flow to additional programs.
Over time, additional modules will be added to the repo to extend NeatSeq-Flow to new and existing programs not yet included.
## Installing and executing NeatSeq-Flow
Please follow the instructions in [the main NeatSeq-Flow repo](https://github.com/bioinfo-core-BGU/neatseq-flow).
## Using the additional modules repo
1. Download and unzip this repo to a location of your choice.
2. Create a [pipeline parameter file](http://neatseq-flow.readthedocs.io/en/latest/02.build_WF.html#parameter-file-definition) using the directions [specified here](http://neatseq-flow.readthedocs.io/en/latest/02.build_WF.html#parameter-file-definition).
3. Add the path to the `module_path` [global parameter](http://neatseq-flow.readthedocs.io/en/latest/02.build_WF.html#global-parameters). (If you have more than one path, you can pass several to the `module_path` as a YAML list).
4. Execute NeatSeq-Flow as [described here](http://neatseq-flow.readthedocs.io/en/latest/02.build_WF.html#execution). Don't forget to pass your pipeline parameter file with the `-p` option.
## Adding your own modules to NeatSeq-Flow
You can easily [write your own modules](http://neatseq-flow.readthedocs.io/en/latest/06.addnew_module.html#for-the-programmer-adding-modules), to include currently unsupported programs in NeatSeq-Flow. Adding these modules is done by adding the local path to the [`module_path`](http://neatseq-flow.readthedocs.io/en/latest/02.build_WF.html#global-parameters) line in the parameter file.
Alternatively, you can add your program without creating a module, [using the `Generic` module](http://neatseq-flow.readthedocs.io/en/latest/modules/generic.html#module-step_classes.Generic.Generic). This enables quickly adding steps to your pipeline without needing to create modules. However, you will need to define the input and output locations in the parameter file. See the [documentation](http://neatseq-flow.readthedocs.io/en/latest/modules/generic.html#module-step_classes.Generic.Generic) for the generic module.
## Contact
Please contact Menachem Sklarz at: [sklarz@bgu.ac.il](mailto:sklarz@bgu.ac.il)
## Citation
When using NeatSeq-Flow, please cite as follows:
Sklarz, M.Y., et al. (2017) **NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows**. [bioRxiv doi: 10.1101/173005](http://www.biorxiv.org/content/early/2017/08/08/173005)